|
|
8f49553d5a
|
First version of the obi test command, testing that the OBITools3 work
correctly
|
2016-09-15 12:26:07 +02:00 |
|
|
|
eb82d088cb
|
Added some view class methods
|
2016-09-05 12:20:00 +02:00 |
|
|
|
8d360b0fac
|
Minor improvements to obi export command
|
2016-08-19 17:49:22 +02:00 |
|
|
|
b34769b27c
|
Minor improvements to obi export command
|
2016-08-19 17:46:55 +02:00 |
|
|
|
2d0a714e37
|
Basic obi export command exporting from view to fasta or fastq format,
for testing purposes
|
2016-08-19 17:40:58 +02:00 |
|
|
|
e4129610cf
|
Quality columns are now optional in NUC_SEQS views + minor fixes
|
2016-08-16 15:17:26 +02:00 |
|
|
|
cf839522e7
|
Minor update and fix to obi grep command
|
2016-08-12 17:45:44 +02:00 |
|
|
|
10b22f79da
|
The cython subclass is now correctly chosen when cloning a view
|
2016-08-12 17:39:19 +02:00 |
|
|
|
ad8e10f2d1
|
Reworked a bit alignment API
|
2016-08-12 15:56:07 +02:00 |
|
|
|
64a745ce0b
|
First very basic version of obi grep command
|
2016-08-11 17:32:08 +02:00 |
|
|
|
d3c58780a0
|
Added __len__ function do OBIViews that returns the line count
|
2016-08-10 17:20:23 +02:00 |
|
|
|
029d395da1
|
Added __iter__ function to OBIView lines
|
2016-08-10 17:08:22 +02:00 |
|
|
|
bea02cc7a5
|
Added (temporary?) check for the type of quality strings because the
import now seems to return them with bytes type
|
2016-08-10 16:25:45 +02:00 |
|
|
|
4ba01617af
|
Fixed obscure compilation bug
|
2016-08-10 15:26:40 +02:00 |
|
|
|
bec684d5e2
|
Fixed merge conflict
|
2016-08-10 15:05:37 +02:00 |
|
|
|
2aaa87edcc
|
1st version of obi align command and reworked functions that handle
column alignment
|
2016-08-10 14:51:02 +02:00 |
|
|
|
400a3f9f3d
|
Merge branch 'Eric_version_for_sequence'
Conflicts:
python/obitools3/obidms/_obidmscolumn_seq.pyx
|
2016-08-04 09:42:42 +02:00 |
|
|
|
d1d26b9028
|
Simplify the code
|
2016-08-04 08:00:54 +02:00 |
|
|
|
465ea81c77
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-08-03 10:13:47 +02:00 |
|
|
|
ccc877764e
|
Patch a bug in the printing of the progress bar leading to a bus error
when compiled with some C compilers and Cython >= 0.24
|
2016-08-03 10:12:23 +02:00 |
|
|
|
8f0462c407
|
Merge branch 'master' into Eric_version_for_sequence
Conflicts:
python/obitools3/obidms/_obidmscolumn_seq.pyx
|
2016-08-03 10:09:20 +02:00 |
|
|
|
26b8e1f215
|
Modified C API to set and get in columns: added functions to set and get
using column names instead of pointers, and changed function names
|
2016-08-02 16:33:19 +02:00 |
|
|
|
312f50ff0f
|
Major update: Column aliases. Columns are now identified in the context
of a view by an alias that can be modified.
|
2016-08-01 18:25:30 +02:00 |
|
|
|
8850e40b6e
|
Minor changes for better presentation
|
2016-07-19 15:30:17 +02:00 |
|
|
|
b89af38109
|
Goes with 38718320
|
2016-07-18 13:57:49 +02:00 |
|
|
|
000b9999ad
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-07-03 09:22:22 +02:00 |
|
|
|
aff9831c13
|
Substitute fprintf call by fputs call to conform with the new ubuntu
compilation rules
|
2016-07-03 09:21:56 +02:00 |
|
|
|
448fa8d325
|
first trial for a fasta formater
|
2016-07-03 09:18:52 +02:00 |
|
|
|
6af62d8124
|
Change a fprintf without argument to a fputs to comply with the new
default parameter on ubuntu
|
2016-07-03 08:25:06 +02:00 |
|
|
|
0869b9ba3f
|
Closes issue #47 by storing each view in a separate file named with the
view's name and created upon view creation.
|
2016-06-30 11:41:30 +02:00 |
|
|
|
38e603ed57
|
Deleted some redundant cython code
|
2016-06-10 10:34:47 +02:00 |
|
|
|
f438c3d913
|
OBIQUAL columns can now handle multiple elements per line
|
2016-06-09 15:54:36 +02:00 |
|
|
|
2a1ea3ba3f
|
Setting NA values is now handled properly for OBI_SEQ, OBI_STR and
OBI_QUAL columns
|
2016-06-09 14:22:36 +02:00 |
|
|
|
69bf7ec2e7
|
NA value for OBI_STR and OBI_SEQ columns is now NULL
|
2016-06-03 18:53:22 +02:00 |
|
|
|
bac7ce7184
|
Start of the implementation of the export methods
|
2016-06-02 19:10:33 +02:00 |
|
|
|
f186395661
|
Trap potential exception generated by char* to bytes casts
|
2016-05-29 21:18:20 +02:00 |
|
|
|
85395dfc1a
|
value returned for sequence is now bytes and no more str
|
2016-05-29 13:53:32 +02:00 |
|
|
|
f830389974
|
Add some comment on the location of the align method.
|
2016-05-29 12:58:31 +02:00 |
|
|
|
2e35229357
|
Add conversion checking on the value of a seq column
|
2016-05-29 12:54:13 +02:00 |
|
|
|
a8ed57dc6e
|
few small changes
|
2016-05-21 12:29:55 +02:00 |
|
|
|
c3274d419c
|
remove an extra debug log
|
2016-05-21 12:29:08 +02:00 |
|
|
|
cca0dbb46b
|
Close issue #54 by adding a read1 method to the MagicKeyFile class
|
2016-05-21 12:24:48 +02:00 |
|
|
|
5a78157112
|
increase parsing speed of the header
|
2016-05-21 10:29:11 +02:00 |
|
|
|
0b9a41d952
|
Patch a bug about the reading of the last sequence
|
2016-05-21 10:28:03 +02:00 |
|
|
|
3b59043ea8
|
Major update: New column type to store sequence qualities. Closes #41
|
2016-05-20 16:45:22 +02:00 |
|
|
|
b3c47809da
|
First version of alignment functions (imported from suma* programs)
|
2016-05-11 16:36:23 +02:00 |
|
|
|
f961621f5d
|
Minor improvements in _obidms Cython layer
|
2016-05-04 13:43:26 +02:00 |
|
|
|
bc12360490
|
Reworked and commented a bit the cython layer for dms, columns and views
|
2016-05-02 15:16:06 +02:00 |
|
|
|
872071b104
|
Removed a list of column pointers kept in the OBIView class that was not
really needed
|
2016-05-02 14:23:42 +02:00 |
|
|
|
baba2d742e
|
commenting _obidms.pyx
|
2016-04-29 16:07:03 +02:00 |
|
